I’m trying to analyze the porosity micro-structure of my bone samples, using Analyze Particles function. When binarized, the structure actually looks very similar to irregularly-shaped cells, which makes it a useful function to measure basic parameters such as the cross-section area (average size), thickness (Feret), and the porosity ratio (Area%) of the bone.
The problem is that the ROI is changing form slide to slide. Using the freehand selection tool, I can draw my desired ROI on each slide, and with the aid of “Interpolate ROI” function, I have my final ROI on each slide. However, it seems that within the ROI manager window, I can only use the basic “measure” function for the selected subset of ROIs. When I use the Analyze particle function, it ignores the created subset, and chooses one fixed ROI for all the stacks! I wonder if I’m missing something? Probably something basic, but I’m not sure what it is.